WEB-THERMODYN: sequence analysis software for profiling DNA helical stability

A sequence analysis system encompassing rules for DNA helical distortion

Recently, it has been shown by Calladine (1982) and Dickerson (1983) that DNA distortions due to steric clashes between opposing purines and pyrimidines can be quantitated based upon four sum functions. The distortions involve helical twist, roll, torsion angle variations and propeller twist. It is the contention of the authors that these perturbations in structure act as information carriers f...

Search Strategies for DNA Sequence Design Software

Designing oligonucleotide sequences that are suitable for applications in nanobiotechnology or DNA Computing is not feasable without the help of computers. Such molecules have to hybridize specifically and with high and homogeneous efficiency to their respective complement. A computer program called dsc (DNA Sequence Compiler) translates specifications of physical, chemical and logical properti...

DNA Sequence Fragment Containing C to A Mutation as a Convenient Mutation Standard for DHPLC Analysis

Objective(s):  Denaturing high performance liquid chromatography (DHPLC) is a high throughput approach for screening DNA sequence variations. To assess oven calibration, cartridge performance, buffer composition and stability, the WAVE Low and High Range Mutation Standards are employed to ensure reproducibility and accuracy of the chromatographic analysis. The purpose of this study was to provi...

Dna Sequence Analysis: the Development of a Custom Software Tool

PhiTM for DNA Sequence Analysis

Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using GPUs, so far not much attention has been paid to the Intel Xeon Phi coprocessor. In this paper we present an algorithm for large-scale DNA analysis that exploit...